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1
Ma, Yuanqing, Elizabeth Hinde, and Katharina Gaus. "Nanodomains in biological membranes." Essays in Biochemistry 57 (February 6, 2015): 93–107. http://dx.doi.org/10.1042/bse0570093.
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Lipid rafts are defined as cholesterol- and sphingomyelin-enriched membrane domains in the plasma membrane of cells that are highly dynamic and cannot be resolved with conventional light microscopy. Membrane proteins that are embedded in the phospholipid matrix can be grouped into raft and non-raft proteins based on their association with detergent-resistant membranes in biochemical assays. Selective lipid–protein interactions not only produce heterogeneity in the membrane, but also cause the spatial compartmentalization of membrane reactions. It has been proposed that lipid rafts function as platforms during cell signalling transduction processes such as T-cell activation (see Chapter 13 (pages 165–175)). It has been proposed that raft association co-localizes specific signalling proteins that may yield the formation of the observed signalling microclusters at the immunological synapses. However, because of the nanometre size and high dynamics of lipid rafts, direct observations have been technically challenging, leading to an ongoing discussion of the lipid raft model and its alternatives. Recent developments in fluorescence imaging techniques have provided new opportunities to investigate the organization of cell membranes with unprecedented spatial resolution. In this chapter, we describe the concept of the lipid raft and alternative models and how new imaging technologies have advanced these concepts.
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Whited, A. M., and A. Johs. "The interactions of peripheral membrane proteins with biological membranes." Chemistry and Physics of Lipids 192 (November 2015): 51–59. http://dx.doi.org/10.1016/j.chemphyslip.2015.07.015.
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Branton, Daniel. "Fracture faces of frozen membranes: 50th anniversary." Molecular Biology of the Cell 27, no. 3 (February 2016): 421–23. http://dx.doi.org/10.1091/mbc.e15-05-0287.
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In 1961, the development of an improved freeze-etching (FE) procedure to prepare rapidly frozen biological cells or tissues for electron microscopy raised two important questions. How does a frozen cell membrane fracture? What do the extensive face views of the cell’s membranes exposed by the fracture process of FE tell us about the overall structure of biological membranes? I discovered that all frozen membranes tend to split along weakly bonded lipid bilayers. Consequently, the fracture process exposes internal membrane faces rather than either of the membrane’s two external surfaces. During etching, when ice is allowed to sublime after fracturing, limited regions of the actual membrane surfaces are revealed. Examination of the fractured faces and etched surfaces provided strong evidence that biological membranes are organized as lipid bilayers with some proteins on the surface and other proteins extending through the bilayer. Membrane splitting made it possible for electron microscopy to show the relative proportion of a membrane’s area that exists in either of these two organizational modes.
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Simunovic, Mijo, and Patricia Bassereau. "Reshaping biological membranes in endocytosis: crossing the configurational space of membrane-protein interactions." Biological Chemistry 395, no. 3 (March 1, 2014): 275–83. http://dx.doi.org/10.1515/hsz-2013-0242.
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Abstract Lipid membranes are highly dynamic. Over several decades, physicists and biologists have uncovered a number of ways they can change the shape of membranes or alter their phase behavior. In cells, the intricate action of membrane proteins drives these processes. Considering the highly complex ways proteins interact with biological membranes, molecular mechanisms of membrane remodeling still remain unclear. When studying membrane remodeling phenomena, researchers often observe different results, leading them to disparate conclusions on the physiological course of such processes. Here we discuss how combining research methodologies and various experimental conditions contributes to the understanding of the entire phase space of membrane-protein interactions. Using the example of clathrin-mediated endocytosis we try to distinguish the question ‘how can proteins remodel the membrane?’ from ‘how do proteins remodel the membrane in the cell?’ In particular, we consider how altering physical parameters may affect the way membrane is remodeled. Uncovering the full range of physical conditions under which membrane phenomena take place is key in understanding the way cells take advantage of membrane properties in carrying out their vital tasks.
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Epand, Richard M. "Membrane Fusion." Bioscience Reports 20, no. 6 (December 1, 2000): 435–41. http://dx.doi.org/10.1023/a:1010498618600.
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The fusion of biological membranes results in two bilayer-based membranes merging into a single membrane. In this process the lipids have to undergo considerable rearrangement. The nature of the intermediates that are formed during this rearrangement has been investigated. Certain fusion proteins facilitate this process. In many cases short segments of these fusion proteins have a particularly important role in accelerating the fusion process. Studies of the interaction of model peptides with membranes have allowed for increased understanding at the molecular level of the mechanism of the promotion of membrane fusion by fusion proteins. There is an increased appreciation of the roles of several independent segments of fusion proteins in promoting the fusion process. Many of the studies of the fusion of biological membranes have been done with the fusion of enveloped viruses with other membranes. One reason for this is that the number of proteins involved in viral fusion is relatively simple, often requiring only a single protein. For many enveloped viruses, the structure of their fusion proteins has certain common elements, suggesting that they all promote fusion by an analogous mechanism. Some aspects of this mechanism also appears to be common to intracellular fusion, although several proteins are involved in that process which is more complex and regulated than is fusion.
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Zhao, Hongxia, and Pekka Lappalainen. "A simple guide to biochemical approaches for analyzing protein–lipid interactions." Molecular Biology of the Cell 23, no. 15 (August 2012): 2823–30. http://dx.doi.org/10.1091/mbc.e11-07-0645.
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Eukaryotic cells contain many different membrane compartments with characteristic shapes, lipid compositions, and dynamics. A large fraction of cytoplasmic proteins associate with these membrane compartments. Such protein–lipid interactions, which regulate the subcellular localizations and activities of peripheral membrane proteins, are fundamentally important for a variety of cell biological processes ranging from cytoskeletal dynamics and membrane trafficking to intracellular signaling. Reciprocally, many membrane-associated proteins can modulate the shape, lipid composition, and dynamics of cellular membranes. Determining the exact mechanisms by which these proteins interact with membranes will be essential to understanding their biological functions. In this Technical Perspective, we provide a brief introduction to selected biochemical methods that can be applied to study protein–lipid interactions. We also discuss how important it is to choose proper lipid composition, type of model membrane, and biochemical assay to obtain reliable and informative data from the lipid-interaction mechanism of a protein of interest.
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MEREZHINSKAYA, Natasha, Gemma A. J. KUIJPERS, and Yossef RAVIV. "Reversible penetration of α-glutathione S-transferase into biological membranes revealed by photosensitized labelling in situ." Biochemical Journal 335, no. 3 (November 1, 1998): 597–604. http://dx.doi.org/10.1042/bj3350597.
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Fluorescent lipid analogue 3,3´-dioctadecyloxacarbocyanine incorporated into biological membranes was used to induce photoactivation of a hydrophobic probe 5-[125I]iodonaphthyl-1-azide (125INA) by energy transfer and to thereby confine subsequent radiolabelling of proteins to the lipid bilayer. This approach was applied in bovine chromaffin cells to discover cytosolic proteins that reversibly penetrate into membrane domains. α-Glutathione S-transferase (α-GST) was identified as the only labelled protein in bovine chromaffin-cell cytosol, indicating that it inserts reversibly into the membrane lipid bilayer. The selectivity of the labelling towards the lipid bilayer is demonstrated by showing that influenza virus haemagglutinin becomes labelled by 125INA only after the insertion of this protein into the target membrane. The molar 125INA:protein ratio was used as a quantitative criterion for evaluation of the penetration of proteins into the membrane lipid bilayer. This ratio was calculated for four integral membrane proteins and four soluble proteins that interact with biological membranes. The values for four integral membrane proteins (erythrocyte anion transporter, multidrug transporter gp-170, dopamine transporter and fusion-competent influenza virus haemagglutinin) were 1, 8, 2 and 2, respectively, whereas for soluble proteins (annexin VII, protein kinase C, BSA and influenza virus haemagglutinin) the values were 0.002, 0, 0.002 and 0.02, respectively. The molar ratio for α-GST was found to be 1, compatible with the values obtained for integral membrane proteins.
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Luchini, Alessandra, and Giuseppe Vitiello. "Mimicking the Mammalian Plasma Membrane: An Overview of Lipid Membrane Models for Biophysical Studies." Biomimetics 6, no. 1 (December 31, 2020): 3. http://dx.doi.org/10.3390/biomimetics6010003.
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Cell membranes are very complex biological systems including a large variety of lipids and proteins. Therefore, they are difficult to extract and directly investigate with biophysical methods. For many decades, the characterization of simpler biomimetic lipid membranes, which contain only a few lipid species, provided important physico-chemical information on the most abundant lipid species in cell membranes. These studies described physical and chemical properties that are most likely similar to those of real cell membranes. Indeed, biomimetic lipid membranes can be easily prepared in the lab and are compatible with multiple biophysical techniques. Lipid phase transitions, the bilayer structure, the impact of cholesterol on the structure and dynamics of lipid bilayers, and the selective recognition of target lipids by proteins, peptides, and drugs are all examples of the detailed information about cell membranes obtained by the investigation of biomimetic lipid membranes. This review focuses specifically on the advances that were achieved during the last decade in the field of biomimetic lipid membranes mimicking the mammalian plasma membrane. In particular, we provide a description of the most common types of lipid membrane models used for biophysical characterization, i.e., lipid membranes in solution and on surfaces, as well as recent examples of their applications for the investigation of protein-lipid and drug-lipid interactions. Altogether, promising directions for future developments of biomimetic lipid membranes are the further implementation of natural lipid mixtures for the development of more biologically relevant lipid membranes, as well as the development of sample preparation protocols that enable the incorporation of membrane proteins in the biomimetic lipid membranes.
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Jacobs, Miranda L., Margrethe A. Boyd, and Neha P. Kamat. "Diblock copolymers enhance folding of a mechanosensitive membrane protein during cell-free expression." Proceedings of the National Academy of Sciences 116, no. 10 (February 13, 2019): 4031–36. http://dx.doi.org/10.1073/pnas.1814775116.
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The expression and integration of membrane proteins into vesicle membranes is a critical step in the design of cell-mimetic biosensors, bioreactors, and artificial cells. While membrane proteins have been integrated into a variety of nonnatural membranes, the effects of the chemical and physical properties of these vesicle membranes on protein behavior remain largely unknown. Nonnatural amphiphiles, such as diblock copolymers, provide an interface that can be synthetically controlled to better investigate this relationship. Here, we focus on the initial step in a membrane protein’s life cycle: expression and folding. We observe improvements in both the folding and overall production of a model mechanosensitive channel protein, the mechanosensitive channel of large conductance, during cell-free reactions when vesicles containing diblock copolymers are present. By systematically tuning the membrane composition of vesicles through incorporation of a poly(ethylene oxide)-b-poly(butadiene) diblock copolymer, we show that membrane protein folding and production can be improved over that observed in traditional lipid vesicles. We then reproduce this effect with an alternate membrane-elasticizing molecule, C12E8. Our results suggest that global membrane physical properties, specifically available membrane surface area and the membrane area expansion modulus, significantly influence the folding and yield of a membrane protein. Furthermore, our results set the stage for explorations into how nonnatural membrane amphiphiles can be used to both study and enhance the production of biological membrane proteins.
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Lee, Sarah C., and Naomi L. Pollock. "Membrane proteins: is the future disc shaped?" Biochemical Society Transactions 44, no. 4 (August 15, 2016): 1011–18. http://dx.doi.org/10.1042/bst20160015.
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The use of styrene maleic acid lipid particles (SMALPs) for the purification of membrane proteins (MPs) is a rapidly developing technology. The amphiphilic copolymer of styrene and maleic acid (SMA) disrupts biological membranes and can extract membrane proteins in nanodiscs of approximately 10 nm diameter. These discs contain SMA, protein and membrane lipids. There is evidence that MPs in SMALPs retain their native structures and functions, in some cases with enhanced thermal stability. In addition, the method is compatible with biological buffers and a wide variety of biophysical and structural analysis techniques. The use of SMALPs to solubilize and stabilize MPs offers a new approach in our attempts to understand, and influence, the structure and function of MPs and biological membranes. In this review, we critically assess progress with this method, address some of the associated technical challenges, and discuss opportunities for exploiting SMA and SMALPs to expand our understanding of MP biology.
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Corey, Robin A., Phillip J. Stansfeld, and Mark S. P. Sansom. "The energetics of protein–lipid interactions as viewed by molecular simulations." Biochemical Society Transactions 48, no. 1 (December 24, 2019): 25–37. http://dx.doi.org/10.1042/bst20190149.
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Membranes are formed from a bilayer containing diverse lipid species with which membrane proteins interact. Integral, membrane proteins are embedded in this bilayer, where they interact with lipids from their surroundings, whilst peripheral membrane proteins bind to lipids at the surface of membranes. Lipid interactions can influence the function of membrane proteins, either directly or allosterically. Both experimental (structural) and computational approaches can reveal lipid binding sites on membrane proteins. It is, therefore, important to understand the free energies of these interactions. This affords a more complete view of the engagement of a particular protein with the biological membrane surrounding it. Here, we describe many computational approaches currently in use for this purpose, including recent advances using both free energy and unbiased simulation methods. In particular, we focus on interactions of integral membrane proteins with cholesterol, and with anionic lipids such as phosphatidylinositol 4,5-bis-phosphate and cardiolipin. Peripheral membrane proteins are exemplified via interactions of PH domains with phosphoinositide-containing membranes. We summarise the current state of the field and provide an outlook on likely future directions of investigation.
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Vogel, Horst. "Structure and dynamics of polypeptides and proteins in lipid membranes." Quarterly Reviews of Biophysics 25, no. 4 (November 1992): 433–57. http://dx.doi.org/10.1017/s0033583500004364.
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The elucidation of the molecular mechanisms whereby ions and polar molecules are translocated across the hydrophobic barrier of a lipid bilayer in biological membranes is one of the most challenging problems in biological research. Specific membrane proteins, such as pumps, carriers and channels, play the central role in the various translocation pathways. Recent progress in expression cloning has provided the sequence of a number of biologically important membrane proteins and in principle the door is open to investigate every protein which might be of importance in the central signal transduction and transport processes. Unfortunately, to date there are only a few examples where the three-dimensional structure of membrane proteins are known at atomic resolution. The photosynthetic reaction centres from purple bacteria (Deisenhoferet al.1985), bacteriorhodopsin (Hendersonet al.1990) and the large porin channel ofRhodobacter capsulata(Weisset al.1991). According to these structural data membrane proteins seem to fold in general in membrane-spanning α-helices and β-strands in order to saturate hydrogen bonds. Only these two motifs seem to form stable structures which can be in contact with the hydrophobic lipid interior of a membrane.
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Karotki, Lena, Juha T. Huiskonen, Christopher J. Stefan, Natasza E. Ziółkowska, Robyn Roth, Michal A. Surma, Nevan J. Krogan, et al. "Eisosome proteins assemble into a membrane scaffold." Journal of Cell Biology 195, no. 5 (November 28, 2011): 889–902. http://dx.doi.org/10.1083/jcb.201104040.
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Spatial organization of membranes into domains of distinct protein and lipid composition is a fundamental feature of biological systems. The plasma membrane is organized in such domains to efficiently orchestrate the many reactions occurring there simultaneously. Despite the almost universal presence of membrane domains, mechanisms of their formation are often unclear. Yeast cells feature prominent plasma membrane domain organization, which is at least partially mediated by eisosomes. Eisosomes are large protein complexes that are primarily composed of many subunits of two Bin–Amphiphysin–Rvs domain–containing proteins, Pil1 and Lsp1. In this paper, we show that these proteins self-assemble into higher-order structures and bind preferentially to phosphoinositide-containing membranes. Using a combination of electron microscopy approaches, we generate structural models of Pil1 and Lsp1 assemblies, which resemble eisosomes in cells. Our data suggest that the mechanism of membrane organization by eisosomes is mediated by self-assembly of its core components into a membrane-bound protein scaffold with lipid-binding specificity.
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Darley, Es, Jasleen Kaur Daljit Singh, Natalie A. Surace, Shelley F. J. Wickham, and Matthew A. B. Baker. "The Fusion of Lipid and DNA Nanotechnology." Genes 10, no. 12 (December 3, 2019): 1001. http://dx.doi.org/10.3390/genes10121001.
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Lipid membranes form the boundary of many biological compartments, including organelles and cells. Consisting of two leaflets of amphipathic molecules, the bilayer membrane forms an impermeable barrier to ions and small molecules. Controlled transport of molecules across lipid membranes is a fundamental biological process that is facilitated by a diverse range of membrane proteins, including ion-channels and pores. However, biological membranes and their associated proteins are challenging to experimentally characterize. These challenges have motivated recent advances in nanotechnology towards building and manipulating synthetic lipid systems. Liposomes—aqueous droplets enclosed by a bilayer membrane—can be synthesised in vitro and used as a synthetic model for the cell membrane. In DNA nanotechnology, DNA is used as programmable building material for self-assembling biocompatible nanostructures. DNA nanostructures can be functionalised with hydrophobic chemical modifications, which bind to or bridge lipid membranes. Here, we review approaches that combine techniques from lipid and DNA nanotechnology to engineer the topography, permeability, and surface interactions of membranes, and to direct the fusion and formation of liposomes. These approaches have been used to study the properties of membrane proteins, to build biosensors, and as a pathway towards assembling synthetic multicellular systems.
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Zhang, Yuliang, Ramya H. Tunuguntla, Pyung-On Choi, and Aleksandr Noy. "Real-time dynamics of carbon nanotube porins in supported lipid membranes visualized by high-speed atomic force microscopy." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1726 (June 19, 2017): 20160226. http://dx.doi.org/10.1098/rstb.2016.0226.
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In-plane mobility of proteins in lipid membranes is one of the fundamental mechanisms supporting biological functionality. Here we use high-speed atomic force microscopy (HS-AFM) to show that a novel type of biomimetic channel—carbon nanotube porins (CNTPs)—is also laterally mobile in supported lipid membranes, mimicking biological protein behaviour. HS-AFM can capture real-time dynamics of CNTP motion in the supported lipid bilayer membrane, build long-term trajectories of the CNTP motion and determine the diffusion coefficients associated with this motion. Our analysis shows that diffusion coefficients of CNTPs fall into the same range as those of proteins in supported lipid membranes. CNTPs in HS-AFM experiments often exhibit ‘directed’ diffusion behaviour, which is common for proteins in live cell membranes. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.
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Thoma, Johannes, and Björn M. Burmann. "Fake It ‘Till You Make It—The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics." International Journal of Molecular Sciences 22, no. 1 (December 23, 2020): 50. http://dx.doi.org/10.3390/ijms22010050.
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Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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Georgieva, Elka R. "Nanoscale lipid membrane mimetics in spin-labeling and electron paramagnetic resonance spectroscopy studies of protein structure and function." Nanotechnology Reviews 6, no. 1 (February 1, 2017): 75–92. http://dx.doi.org/10.1515/ntrev-2016-0080.
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AbstractCellular membranes and associated proteins play critical physiological roles in organisms from all life kingdoms. In many cases, malfunction of biological membranes triggered by changes in the lipid bilayer properties or membrane protein functional abnormalities lead to severe diseases. To understand in detail the processes that govern the life of cells and to control diseases, one of the major tasks in biological sciences is to learn how the membrane proteins function. To do so, a variety of biochemical and biophysical approaches have been used in molecular studies of membrane protein structure and function on the nanoscale. This review focuses on electron paramagnetic resonance with site-directed nitroxide spin-labeling (SDSL EPR), which is a rapidly expanding and powerful technique reporting on the local protein/spin-label dynamics and on large functionally important structural rearrangements. On the other hand, adequate to nanoscale study membrane mimetics have been developed and used in conjunction with SDSL EPR. Primarily, these mimetics include various liposomes, bicelles, and nanodiscs. This review provides a basic description of the EPR methods, continuous-wave and pulse, applied to spin-labeled proteins, and highlights several representative applications of EPR to liposome-, bicelle-, or nanodisc-reconstituted membrane proteins.
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Era, Seiichi. "Protein Translocation across Biological Membranes and Molten Globule State on Globular Proteins." membrane 18, no. 6 (1993): 318–24. http://dx.doi.org/10.5360/membrane.18.318.
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Yeh, Vivien, Alice Goode, and Boyan B. Bonev. "Membrane Protein Structure Determination and Characterisation by Solution and Solid-State NMR." Biology 9, no. 11 (November 12, 2020): 396. http://dx.doi.org/10.3390/biology9110396.
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Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise key functional interactions with lipids, small molecules and membrane modulators, as well as their conformational polymorphism and dynamics. NMR is uniquely suited to resolving atomic environments within complex molecular assemblies and reporting on membrane organisation, protein structure, lipid and polysaccharide composition, conformational variations and molecular interactions. The main challenge in membrane protein studies at the atomic level remains the need for a membrane environment to support their fold. NMR studies in membrane mimetics and membranes of increasing complexity offer close to native environments for structural and molecular studies of membrane proteins. Solution NMR inherits high resolution from small molecule analysis, providing insights from detergent solubilised proteins and small molecular assemblies. Solid-state NMR achieves high resolution in membrane samples through fast sample spinning or sample alignment. Recent developments in dynamic nuclear polarisation NMR allow signal enhancement by orders of magnitude opening new opportunities for expanding the applications of NMR to studies of native membranes and whole cells.
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Matos, Anna Lívia Linard, Sergej Kudruk, Johanna Moratz, Milena Heflik, David Grill, Bart Jan Ravoo, and Volker Gerke. "Membrane Binding Promotes Annexin A2 Oligomerization." Cells 9, no. 5 (May 8, 2020): 1169. http://dx.doi.org/10.3390/cells9051169.
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Annexin A2 (AnxA2) is a cytosolic Ca2+ regulated membrane binding protein that can induce lipid domain formation and plays a role in exocytosis and endocytosis. To better understand the mode of annexin-membrane interaction, we analyzed membrane-bound AnxA2 assemblies by employing a novel 3-armed chemical crosslinker and specific AnxA2 mutant proteins. Our data show that AnxA2 forms crosslinkable oligomers upon binding to membranes containing negatively charged phospholipids. AnxA2 mutants with amino acid substitutions in residues predicted to be involved in lateral protein–protein interaction show compromised oligomer formation, albeit still being capable of binding to negatively charged membranes in the presence of Ca2+. These results suggest that lateral protein–protein interactions are involved in the formation of AnxA2 clusters on a biological membrane.
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Huang, Haihong, Baosheng Ge, Shuai Zhang, Jiqiang Li, Chenghao Sun, Tongtao Yue, and Fang Huang. "Using Fluorescence Quenching Titration to Determine the Orientation of a Model Transmembrane Protein in Mimic Membranes." Materials 12, no. 3 (January 23, 2019): 349. http://dx.doi.org/10.3390/ma12030349.
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After synthesis of transmembrane proteins (TMPs), they are transferred and inserted into plasma membranes to play biological functions. Crucially, orientation of TMPs in membranes determines whether they have biological activities. In cellular environments, a number of cofactors, such as translocon, can assist TMPs to be inserted into membranes in defined orientations. During in vitro reconstitution of TMPs with mimic membranes, both insertion and orientation of TMPs are primarily determined by interactions with the membrane. Yet the knowledge is limited, hindering the in vitro applications of TMPs. Here, we take Bacteriorhodopsin (bR) as a model TMP, using fluorescence quenching titration experiment to identify orientation of bR in mimic membranes, examining effects of a number of factors, including lipid composition, pH value, ionic strength and membrane curvature. The most effective determinant is the lipid type, which modulates insertion and orientation of bR in membranes by changing the membrane surface charge and the membrane fluidity. Both the pH value and the ionic strength play secondary roles by tuning the nature of the electrostatic interaction. The membrane curvature was found to have a minor effect on orientation of bR in membranes. By comparing orientations of bR in folded and unfolded states, no obvious change was observed, informing that nascent proteins could be inserted into membranes in defined orientations before folding into the native state inside the membrane.
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Mandala, Venkata S., Jonathan K. Williams, and Mei Hong. "Structure and Dynamics of Membrane Proteins from Solid-State NMR." Annual Review of Biophysics 47, no. 1 (May 20, 2018): 201–22. http://dx.doi.org/10.1146/annurev-biophys-070816-033712.
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Solid-state nuclear magnetic resonance (SSNMR) spectroscopy elucidates membrane protein structures and dynamics in atomic detail to yield mechanistic insights. By interrogating membrane proteins in phospholipid bilayers that closely resemble biological membranes, SSNMR spectroscopists have revealed ion conduction mechanisms, substrate transport dynamics, and oligomeric interfaces of seven-transmembrane helix proteins. Research has also identified conformational plasticity underlying virus-cell membrane fusions by complex protein machineries, and β-sheet folding and assembly by amyloidogenic proteins bound to lipid membranes. These studies collectively show that membrane proteins exhibit extensive structural plasticity to carry out their functions. Because of the inherent dependence of NMR frequencies on molecular orientations and the sensitivity of NMR frequencies to dynamical processes on timescales from nanoseconds to seconds, SSNMR spectroscopy is ideally suited to elucidate such structural plasticity, local and global conformational dynamics, protein-lipid and protein-ligand interactions, and protonation states of polar residues. New sensitivity-enhancement techniques, resolution enhancement by ultrahigh magnetic fields, and the advent of 3D and 4D correlation NMR techniques are increasingly aiding these mechanistically important structural studies.
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Nastou, Katerina C., Georgios N. Tsaousis, Kimon E. Kremizas, Zoi I. Litou, and Stavros J. Hamodrakas. "The Human Plasma Membrane Peripherome: Visualization and Analysis of Interactions." BioMed Research International 2014 (2014): 1–12. http://dx.doi.org/10.1155/2014/397145.
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A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with noncovalent interactions. The aim of this study was to construct and analyze the interactions of the human plasma membrane peripheral proteins (peripherome hereinafter). For this purpose, we collected a dataset of peripheral proteins of the human plasma membrane. We also collected a dataset of experimentally verified interactions for these proteins. The interaction network created from this dataset has been visualized using Cytoscape. We grouped the proteins based on their subcellular location and clustered them using the MCL algorithm in order to detect functional modules. Moreover, functional and graph theory based analyses have been performed to assess biological features of the network. Interaction data with drug molecules show that ~10% of peripheral membrane proteins are targets for approved drugs, suggesting their potential implications in disease. In conclusion, we reveal novel features and properties regarding the protein-protein interaction network created by peripheral proteins of the human plasma membrane.
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Andreu-Fernández, Vicente, Mónica Sancho, Ainhoa Genovés, Estefanía Lucendo, Franziska Todt, Joachim Lauterwasser, Kathrin Funk, et al. "Bax transmembrane domain interacts with prosurvival Bcl-2 proteins in biological membranes." Proceedings of the National Academy of Sciences 114, no. 2 (December 27, 2016): 310–15. http://dx.doi.org/10.1073/pnas.1612322114.
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The Bcl-2 (B-cell lymphoma 2) protein Bax (Bcl-2 associated X, apoptosis regulator) can commit cells to apoptosis via outer mitochondrial membrane permeabilization. Bax activity is controlled in healthy cells by prosurvival Bcl-2 proteins. C-terminal Bax transmembrane domain interactions were implicated recently in Bax pore formation. Here, we show that the isolated transmembrane domains of Bax, Bcl-xL (B-cell lymphoma-extra large), and Bcl-2 can mediate interactions between Bax and prosurvival proteins inside the membrane in the absence of apoptotic stimuli. Bcl-2 protein transmembrane domains specifically homooligomerize and heterooligomerize in bacterial and mitochondrial membranes. Their interactions participate in the regulation of Bcl-2 proteins, thus modulating apoptotic activity. Our results suggest that interactions between the transmembrane domains of Bax and antiapoptotic Bcl-2 proteins represent a previously unappreciated level of apoptosis regulation.
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Xing You, Hong, Xiaoyang Qi, and Lei Yu. "Real-Time Observation of Phospholipid Bilayer Membrane Restructuring Induced by Protein Molecules using Atomic Force Microscopy." Microscopy and Microanalysis 7, S2 (August 2001): 858–59. http://dx.doi.org/10.1017/s1431927600030361.
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Atomic force microscopy (AFM) allows the surfaces of native biological materials to be imaged in aqueous solution with submolecular resolution. The ability to perform AFM imaging in aqueous and physiological environment has made it possible to monitor important biological processes in real time at high resolution. Currently, there is a great deal of interest in AFM studies of the structure and property of lipid bilayer membranes and protein interactions with lipid bilayer membranes. Lipid bilayer membranes in biological cells form a permeability barrier, which controls the flow of ions, water, and other molecules between biological cells and their environments, whereas membrane-bound and/or membrane-associated proteins are responsible for most of the dynamic functions carried out by the membrane. However, real-time AFM monitoring of dynamic biological processes has been challenged by the limited temporal resolution of AFM, potential physical damage to soft biological samples, and intrinsic complexity of biological processes. There are few successful examples of AFM real-time studies of dynamic biological events, particularly in the aspect of protein interactions with lipid bilayer membranes.We have attempted to use atomic force microscopy to study interactions between a particular protein, saposin C, and phospholipid bilayer membranes in real time. Saposin C (Sap C), a small glycoprotein, is an essential co-factor for the hydrolysis of glucosylceramide by glucosylceramidase in lysosomes, and a deficiency of Sap C leads to a variant form of Gauchers’ diseases. Supported planar phospholipid bilayer membranes were used in the study.
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Booth, Paula J., A. Rachael Curran, Richard H. Templer, Hui Lu, and Wim Meijberg. "Manipulating the folding of membrane proteins: using the bilayer to our advantage." Biochemical Society Symposia 68 (August 1, 2001): 27–33. http://dx.doi.org/10.1042/bss0680027.
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The folding mechanisms of integral membrane proteins have largely eluded detailed study. This is owing to the inherent difficulties in folding these hydrophobic proteins in vitro, which, in turn, reflects the often apparently insurmountable problem of mimicking the natural membrane bilayer with lipid or detergent mixtures. There is, however, a large body of information on lipid properties and, in particular, on phosphatidylcholine and phosphatidylethanolamine lipids, which are common to many biological membranes. We have exploited this knowledge to develop efficient in vitro lipid-bilayer folding systems for the membrane protein, bacteriorhodopsin. Furthermore, we have shown that a rate-limiting apoprotein folding step and the overall folding efficiency appear to be controlled by particular properties of the lipid bilayer. The properties of interest are the stored curvature elastic energy within the bilayer, and the lateral pressure that the lipid chains exert on the their neighbouring folding proteins. These are generic properties of the bilayer that can be achieved with simple mixtures of biological lipids, and are not specific to the lipids studied here. These bilayer properties also seem to be important in modulating the function of several membrane proteins, as well as the function of membranes in vivo. Thus, it seems likely that careful manipulations of lipid properties will shed light on the forces that drive membrane protein folding, and will aid the development of bilayer folding systems for other membrane proteins.
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Guo, Qi, Lei Liu, Won C. Yim, John C. Cushman, and Bronwyn J. Barkla. "Membrane Profiling by Free Flow Electrophoresis and SWATH-MS to Characterize Subcellular Compartment Proteomes in Mesembryanthemum crystallinum." International Journal of Molecular Sciences 22, no. 9 (May 9, 2021): 5020. http://dx.doi.org/10.3390/ijms22095020.
Full textAbstract:
The study of subcellular membrane structure and function facilitates investigations into how biological processes are divided within the cell. However, work in this area has been hampered by the limited techniques available to fractionate the different membranes. Free Flow Electrophoresis (FFE) allows for the fractionation of membranes based on their different surface charges, a property made up primarily of their varied lipid and protein compositions. In this study, high-resolution plant membrane fractionation by FFE, combined with mass spectrometry-based proteomics, allowed the simultaneous profiling of multiple cellular membranes from the leaf tissue of the plant Mesembryanthemum crystallinum. Comparisons of the fractionated membranes’ protein profile to that of known markers for specific cellular compartments sheds light on the functions of proteins, as well as provides new evidence for multiple subcellular localization of several proteins, including those involved in lipid metabolism.
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Botterbusch, Samuel, and Tobias Baumgart. "Interactions between Phase-Separated Liquids and Membrane Surfaces." Applied Sciences 11, no. 3 (January 31, 2021): 1288. http://dx.doi.org/10.3390/app11031288.
Full textAbstract:
Liquid-liquid phase separation has recently emerged as an important fundamental organizational phenomenon in biological settings. Most studies of biological phase separation have focused on droplets that “condense” from solution above a critical concentration, forming so-called “membraneless organelles” suspended in solution. However, membranes are ubiquitous throughout cells, and many biomolecular condensates interact with membrane surfaces. Such membrane-associated phase-separated systems range from clusters of integral or peripheral membrane proteins in the plane of the membrane to free, spherical droplets wetting membrane surfaces to droplets containing small lipid vesicles. In this review, we consider phase-separated liquids that interact with membrane surfaces and we discuss the consequences of those interactions. The physical properties of distinct liquid phases in contact with bilayers can reshape the membrane, and liquid-liquid phase separation can construct membrane-associated protein structures, modulate their function, and organize collections of lipid vesicles dynamically. We summarize the common phenomena that arise in these systems of liquid phases and membranes.
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Subczynski, W. K., and A. Wisniewska. "Physical properties of lipid bilayer membranes: relevance to membrane biological functions." Acta Biochimica Polonica 47, no. 3 (September 30, 2000): 613–25. http://dx.doi.org/10.18388/abp.2000_3983.
Full textAbstract:
Over the last 25 years one of us (WKS) has been investigating physical properties of lipid bilayer membranes. In 1991 a group led by WKS was organized into the Laboratory of Structure and Dynamics of Biological Membranes, the effective member of which is AW. Using mainly the electron paramagnetic resonance (EPR) spin-labeling method, we obtained unexpected results, which are significant for the better understanding of the functioning of biological membranes. We have developed a new pulse EPR spin-labeling method for the detection of membrane domains and evaluation of lipid exchange rates. This review will be focused on our main results which can be summarized as follows: (1) Unsaturation of alkyl chains greatly reduces the ordering and rigidifying effects of cholesterol although the unsaturation alone gives only minor fluidizing effects, as observed by order and reorientational motion, and rather significant rigidifying effects, as observed by translational motion of probe molecules; (2) Fluid-phase model membranes and cell plasma membranes are not barriers to oxygen and nitric oxide transport; (3) Polar carotenoids can regulate membrane fluidity in a way similar to cholesterol; (4) Formation of effective hydrophobic barriers to the permeation of small polar molecules across membranes requires alkyl chain unsaturation and/or the presence of cholesterol; (5) Fluid-phase micro-immiscibility takes place in cis-unsaturated phosphatidylcholine-cholesterol membranes and induces the formation of cholesterol-rich domains; (6) In membranes containing high concentrations of transmembrane proteins a new lipid domain is formed, with lipids trapped within aggregates of proteins, in which the lipid dynamics is diminished to the level of gel-phase.
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Puth, Kristina, Harald F. Hofbauer, James P. Sáenz, and Robert Ernst. "Homeostatic control of biological membranes by dedicated lipid and membrane packing sensors." Biological Chemistry 396, no. 9-10 (September 1, 2015): 1043–58. http://dx.doi.org/10.1515/hsz-2015-0130.
Full textAbstract:
Abstract Biological membranes are dynamic and complex assemblies of lipids and proteins. Eukaryotic lipidomes encompass hundreds of distinct lipid species and we have only begun to understand their role and function. This review focuses on recent advances in the field of lipid sensors and discusses methodical approaches to identify and characterize putative sensor domains. We elaborate on the role of integral and conditionally membrane-associated sensor proteins, their molecular mechanisms, and identify open questions in the emerging field of membrane homeostasis.
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Willems, Kherim, Veerle Van Meervelt, Carsten Wloka, and Giovanni Maglia. "Single-molecule nanopore enzymology." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1726 (June 19, 2017): 20160230. http://dx.doi.org/10.1098/rstb.2016.0230.
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Biological nanopores are a class of membrane proteins that open nanoscale water conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. In addition, a more recent nanopore application is the analysis of single proteins and enzymes. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here, we describe the approaches and challenges in nanopore enzymology. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.
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Xu, Yan, Victor E. Yushmanov, and Pei Tang. "NMR Studies of Drug Interaction with Membranes and Membrane-Associated Proteins." Bioscience Reports 22, no. 2 (April 1, 2002): 175–96. http://dx.doi.org/10.1023/a:1020182404940.
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This review focuses on the recent developments in the study of drug interactions with biological membranes and membrane-associated proteins using nuclear magnetic resonance (NMR) spectroscopy and other spectroscopic techniques. Emphasis is placed on a class of low-affinity neurological agents as exemplified by volatile general anesthetics and structurally related compounds. The technical aspects are reviewed of how to prepare membrane-mimetic systems and of NMR approaches that are either in current use or opening new prospects. A brief literature survey covers studies ranging from drug distribution in simplified lipid matrix to specific drug interaction with neuronal receptors reconstituted in complicated synthetic membrane systems.
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Levi, Valeria, Ana M. Villamil Giraldo, Pablo R. Castello, Juan P. F. C. Rossi, and F. Luis González Flecha. "Effects of phosphatidylethanolamine glycation on lipid–protein interactions and membrane protein thermal stability." Biochemical Journal 416, no. 1 (October 28, 2008): 145–52. http://dx.doi.org/10.1042/bj20080618.
Full textAbstract:
Non-enzymatic glycation of biomolecules has been implicated in the pathophysiology of aging and diabetes. Among the potential targets for glycation are biological membranes, characterized by a complex organization of lipids and proteins interacting and forming domains of different size and stability. In the present study, we analyse the effects of glycation on the interactions between membrane proteins and lipids. The phospholipid affinity for the transmembrane surface of the PMCA (plasma-membrane Ca2+-ATPase) was determined after incubating the protein or the phospholipids with glucose. Results show that the affinity between PMCA and the surrounding phospholipids decreases significantly after phosphospholipid glycation, but remains unmodified after glycation of the protein. Furthermore, phosphatidylethanolamine glycation decreases by ∼30% the stability of PMCA against thermal denaturation, suggesting that glycated aminophospholipids induce a structural rearrangement in the protein that makes it more sensitive to thermal unfolding. We also verified that lipid glycation decreases the affinity of lipids for two other membrane proteins, suggesting that this effect might be common to membrane proteins. Extending these results to the in vivo situation, we can hypothesize that, under hyperglycaemic conditions, glycation of membrane lipids may cause a significant change in the structure and stability of membrane proteins, which may affect the normal functioning of membranes and therefore of cells.
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Hu, Ping, Susan Meyers, Feng-Xia Liang, Fang-Ming Deng, Bechara Kachar, Mark L. Zeidel, and Tung-Tien Sun. "Role of membrane proteins in permeability barrier function: uroplakin ablation elevates urothelial permeability." American Journal of Physiology-Renal Physiology 283, no. 6 (December 1, 2002): F1200—F1207. http://dx.doi.org/10.1152/ajprenal.00043.2002.
Full textAbstract:
Although water, small nonelectrolytes, and gases are freely permeable through most biological membranes, apical membranes of certain barrier epithelia exhibit extremely low permeabilities to these substances. The role of integral membrane proteins in this barrier function has been unclear. To study this problem, we have ablated the mouse gene encoding uroplakin III (UPIII), one of the major protein subunits in urothelial apical membranes, and measured the permeabilities of these membranes. Ablation of the UPIII gene greatly diminishes the amounts of uroplakins on the apical urothelial membrane (Hu P, Deng FM, Liang FX, Hu CM, Auerbach AB, Shapiro E, Wu XR, Kachar B, and Sun TT. J Cell Biol151: 961–972, 2000). Our results indicate that normal mouse urothelium exhibits high transepithelial resistance and low urea and water permeabilities. The UPIII-deficient urothelium exhibits a normal transepithelial resistance (normal 2,024 ± 122, knockout 2,322 ± 114 Ω · cm2; P > 0.5). However, the UPIII-deficient apical membrane has a significantly elevated water permeability (normal 0.91 ± 0.06, knockout 1.83 ± 0.14 cm/s × 10−5; P < 0.05). The urea permeability of the UPIII-deficient membrane also increased, although to a lesser extent (normal 2.22 ± 0.24, knockout 2.93 ± 0.31 cm/s × 10−6; P = 0.12). These results indicate that reduced targeting of uroplakins to the apical membrane does not significantly alter the tight junctional barrier but does double the water permeability. We provide the first demonstration that integral membrane proteins contribute to the apical membrane permeability barrier function of urothelium.
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Tanaka, Motomu. "Polymer-Supported Membranes: Physical Models of Cell Surfaces." MRS Bulletin 31, no. 7 (July 2006): 513–20. http://dx.doi.org/10.1557/mrs2006.135.
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The functional modification of solid surfaces with plasma membrane models has been drawing increasing attention as a straightforward strategy to bridge soft biological materials and hard inorganic materials. Planar model membranes can be deposited either directly on solid substrates (solid-supported membranes), or on ultrathin polymer supports (polymer-supported membranes) that mimic the generic role of the extracellular matrix and the cell surface. The first part of this review provides an overview of advances in the fabrication of polymer-supported membranes. The middle section describes how such thin polymer interlayers can physically modulate the membrane–substrate contact. The last section introduces several methods to localize membranes and membrane proteins. Finally, some ideas are presented on combining supported membrane concepts with semiconductor technology toward applications in materials science.
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Benhaim, Mark A., and Kelly K. Lee. "New Biophysical Approaches Reveal the Dynamics and Mechanics of Type I Viral Fusion Machinery and Their Interplay with Membranes." Viruses 12, no. 4 (April 8, 2020): 413. http://dx.doi.org/10.3390/v12040413.
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Protein-mediated membrane fusion is a highly regulated biological process essential for cellular and organismal functions and infection by enveloped viruses. During viral entry the membrane fusion reaction is catalyzed by specialized protein machinery on the viral surface. These viral fusion proteins undergo a series of dramatic structural changes during membrane fusion where they engage, remodel, and ultimately fuse with the host membrane. The structural and dynamic nature of these conformational changes and their impact on the membranes have long-eluded characterization. Recent advances in structural and biophysical methodologies have enabled researchers to directly observe viral fusion proteins as they carry out their functions during membrane fusion. Here we review the structure and function of type I viral fusion proteins and mechanisms of protein-mediated membrane fusion. We highlight how recent technological advances and new biophysical approaches are providing unprecedented new insight into the membrane fusion reaction.
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Marsh, Derek. "Interactions at the Membrane Surface Studied by Spin Label ESR Spectroscopy." Bioscience Reports 19, no. 4 (August 1, 1999): 253–59. http://dx.doi.org/10.1023/a:1020590122846.
Full textAbstract:
A range of different types of interactions at biological membrane surfaces have been studied using various different spin label electron spin resonance (ESR) techniques. These include: (1) the interfacial ionization of local anaesthetics, (2) the binding of peripheral membrane proteins, (3) the membrane insertion of translocation-competent precursor proteins and other components of the protein translocation machinery, (4) the interactions of ganglioside sphingolipids with membrane proteins, and (5) the specific surface recognition of biotinylated phospholipid headgroups by avidin. A description of these illustrates both the capabilities of this biophysical methodology and the functional/technological implications of these interactions and dynamic/thermodynamic processes for cell membranes and their surfaces.
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Sejwal, Kushal, Mohamed Chami, Paul Baumgartner, Julia Kowal, Shirley A. Müller, and Henning Stahlberg. "Proteoliposomes – a system to study membrane proteins under buffer gradients by cryo-EM." Nanotechnology Reviews 6, no. 1 (February 1, 2017): 57–74. http://dx.doi.org/10.1515/ntrev-2016-0081.
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AbstractMembrane proteins are vital to life and major therapeutic targets. Yet, understanding how they function is limited by a lack of structural information. In biological cells, membrane proteins reside in lipidic membranes and typically experience different buffer conditions on both sides of the membrane or even electric potentials and transmembrane gradients across the membranes. Proteoliposomes, which are lipidic vesicles filled with reconstituted membrane proteins, provide an ideal model system for structural and functional studies of membrane proteins under conditions that mimic nature to a certain degree. We discuss methods for the formation of liposomes and proteoliposomes, their imaging by cryo-electron microscopy, and the structural analysis of proteins present in their bilayer. We suggest the formation of ordered arrays akin to weakly ordered two-dimensional (2D) crystals in the bilayer of liposomes as a means to achieve high-resolution, and subsequent buffer modification as a method to capture snapshots of membrane proteins in action.
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Misawa, Nobuo, Toshihisa Osaki, and Shoji Takeuchi. "Membrane protein-based biosensors." Journal of The Royal Society Interface 15, no. 141 (April 2018): 20170952. http://dx.doi.org/10.1098/rsif.2017.0952.
Full textAbstract:
This review highlights recent development of biosensors that use the functions of membrane proteins. Membrane proteins are essential components of biological membranes and have a central role in detection of various environmental stimuli such as olfaction and gustation. A number of studies have attempted for development of biosensors using the sensing property of these membrane proteins. Their specificity to target molecules is particularly attractive as it is significantly superior to that of traditional human-made sensors. In this review, we classified the membrane protein-based biosensors into two platforms: the lipid bilayer-based platform and the cell-based platform. On lipid bilayer platforms, the membrane proteins are embedded in a lipid bilayer that bridges between the protein and a sensor device. On cell-based platforms, the membrane proteins are expressed in a cultured cell, which is then integrated in a sensor device. For both platforms we introduce the fundamental information and the recent progress in the development of the biosensors, and remark on the outlook for practical biosensing applications.
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Saarikangas, Juha, Hongxia Zhao, and Pekka Lappalainen. "Regulation of the Actin Cytoskeleton-Plasma Membrane Interplay by Phosphoinositides." Physiological Reviews 90, no. 1 (January 2010): 259–89. http://dx.doi.org/10.1152/physrev.00036.2009.
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The plasma membrane and the underlying cortical actin cytoskeleton undergo continuous dynamic interplay that is responsible for many essential aspects of cell physiology. Polymerization of actin filaments against cellular membranes provides the force for a number of cellular processes such as migration, morphogenesis, and endocytosis. Plasma membrane phosphoinositides (especially phosphatidylinositol bis- and trisphosphates) play a central role in regulating the organization and dynamics of the actin cytoskeleton by acting as platforms for protein recruitment, by triggering signaling cascades, and by directly regulating the activities of actin-binding proteins. Furthermore, a number of actin-associated proteins, such as BAR domain proteins, are capable of directly deforming phosphoinositide-rich membranes to induce plasma membrane protrusions or invaginations. Recent studies have also provided evidence that the actin cytoskeleton-plasma membrane interactions are misregulated in a number of pathological conditions such as cancer and during pathogen invasion. Here, we summarize the wealth of knowledge on how the cortical actin cytoskeleton is regulated by phosphoinositides during various cell biological processes. We also discuss the mechanisms by which interplay between actin dynamics and certain membrane deforming proteins regulate the morphology of the plasma membrane.
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Erwin, Nelli, Satyajit Patra, Mridula Dwivedi, Katrin Weise, and Roland Winter. "Influence of isoform-specific Ras lipidation motifs on protein partitioning and dynamics in model membrane systems of various complexity." Biological Chemistry 398, no. 5-6 (May 1, 2017): 547–63. http://dx.doi.org/10.1515/hsz-2016-0289.
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Abstract The partitioning of the lipidated signaling proteins N-Ras and K-Ras4B into various membrane systems, ranging from single-component fluid bilayers, binary fluid mixtures, heterogeneous raft model membranes up to complex native-like lipid mixtures (GPMVs) in the absence and presence of integral membrane proteins have been explored in the last decade in a combined chemical-biological and biophysical approach. These studies have revealed pronounced isoform-specific differences regarding the lateral distribution in membranes and formation of protein-rich membrane domains. In this context, we will also discuss the effects of lipid head group structure and charge density on the partitioning behavior of the lipoproteins. Moreover, the dynamic properties of N-Ras and K-Ras4B have been studied in different model membrane systems and native-like crowded milieus. Addition of crowding agents such as Ficoll and its monomeric unit, sucrose, gradually favors clustering of Ras proteins in forming small oligomers in the bulk; only at very high crowder concentrations association is disfavored.
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Iwasaki, Yukimoto, Takafumi Itoh, Yusuke Hagi, Sakura Matsuta, Aki Nishiyama, Genki Chaya, Yuki Kobayashi, Kotaro Miura, and Setsuko Komatsu. "Proteomics Analysis of Plasma Membrane Fractions of the Root, Leaf, and Flower of Rice." International Journal of Molecular Sciences 21, no. 19 (September 23, 2020): 6988. http://dx.doi.org/10.3390/ijms21196988.
Full textAbstract:
The plasma membrane regulates biological processes such as ion transport, signal transduction, endocytosis, and cell differentiation/proliferation. To understand the functional characteristics and organ specificity of plasma membranes, plasma membrane protein fractions from rice root, etiolated leaf, green leaf, developing leaf sheath, and flower were analyzed by proteomics. Among the proteins identified, 511 were commonly accumulated in the five organs, whereas 270, 132, 359, 146, and 149 proteins were specifically accumulated in the root, etiolated leaf, green leaf, developing leaf sheath, and developing flower, respectively. The principle component analysis revealed that the functions of the plasma membrane in the root was different from those of green and etiolated leaves and that the plasma membrane protein composition of the leaf sheath was similar to that of the flower, but not that of the green leaf. Functional classification revealed that the root plasma membrane has more transport-related proteins than the leaf plasma membrane. Furthermore, the leaf sheath and flower plasma membranes were found to be richer in proteins involved in signaling and cell function than the green leaf plasma membrane. To validate the proteomics data, immunoblot analysis was carried out, focusing on four heterotrimeric G protein subunits, Gα, Gβ, Gγ1, and Gγ2. All subunits could be detected by both methods and, in particular, Gγ1 and Gγ2 required concentration by immunoprecipitation for mass spectrometry detection.
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Gov, N. S. "Guided by curvature: shaping cells by coupling curved membrane proteins and cytoskeletal forces." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1747 (April 9, 2018): 20170115. http://dx.doi.org/10.1098/rstb.2017.0115.
Full textAbstract:
Eukaryote cells have flexible membranes that allow them to have a variety of dynamical shapes. The shapes of the cells serve important biological functions, both for cells within an intact tissue, and during embryogenesis and cellular motility. How cells control their shapes and the structures that they form on their surface has been a subject of intensive biological research, exposing the building blocks that cells use to deform their membranes. These processes have also drawn the interest of theoretical physicists, aiming to develop models based on physics, chemistry and nonlinear dynamics. Such models explore quantitatively different possible mechanisms that the cells can employ to initiate the spontaneous formation of shapes and patterns on their membranes. We review here theoretical work where one such class of mechanisms was investigated: the coupling between curved membrane proteins, and the cytoskeletal forces that they recruit. Theory indicates that this coupling gives rise to a rich variety of membrane shapes and dynamics, while experiments indicate that this mechanism appears to drive many cellular shape changes. This article is part of the theme issue ‘Self-organization in cell biology’.
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Sondhi, Palak, Dhanbir Lingden, and Keith J. Stine. "Structure, Formation, and Biological Interactions of Supported Lipid Bilayers (SLB) Incorporating Lipopolysaccharide." Coatings 10, no. 10 (October 14, 2020): 981. http://dx.doi.org/10.3390/coatings10100981.
Full textAbstract:
Biomimetic membrane systems play a crucial role in the field of biosensor engineering. Over the years, significant progress has been achieved creating artificial membranes by various strategies from vesicle fusion to Langmuir transfer approaches to meet an ever-growing demand for supported lipid bilayers on various substrates such as glass, mica, gold, polymer cushions, and many more. This paper reviews the diversity seen in the preparation of biologically relevant model lipid membranes which includes monolayers and bilayers of phospholipid and other crucial components such as proteins, characterization techniques, changes in the physical properties of the membranes during molecular interactions and the dynamics of the lipid membrane with biologically active molecules with special emphasis on lipopolysaccharides (LPS).
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Lipowsky, Reinhard. "Remodeling of membrane compartments: some consequences of membrane fluidity." Biological Chemistry 395, no. 3 (March 1, 2014): 253–74. http://dx.doi.org/10.1515/hsz-2013-0244.
Full textAbstract:
Abstract Biological membranes consist of fluid bilayers with many lipid and protein components. This fluidity implies a high flexibility that allows the membranes to attain a large variety of different shapes. One important shape parameter is the spontaneous curvature, which describes the asymmetry between the two leaflets of a bilayer and can be changed by adsorption of ‘particles’ such as ions or proteins from the aqueous phases. Membrane fluidity also implies that the membranes can change their local composition via lateral diffusion and form intramembrane compartments. Two mechanisms for the formation of such compartments can be distinguished: membrane segmentation arising from structured environments and domain formation as a result of phase separation within the membranes. The interplay between these two mechanisms provides a simple and generic explanation for the difficulty to observe phase domains in vivo. Intramembrane domains can form new membrane compartments via budding and tubulation processes. Which of these two processes actually occurs depends on the fluid-elastic properties of the domains, on the adsorption kinetics, and on external constraints arising, e.g., from the osmotic conditions. Vesicles are predicted to unbind from adhesive surfaces via tubulation when the spontaneous curvature of their membranes exceeds a certain threshold value.
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Serrano, R., and C. Montesinos. "Molecular Bases of Desiccation Tolerance in Plant Cells and Potential Applications in Food Dehydration." Food Science and Technology International 9, no. 3 (June 2003): 157–61. http://dx.doi.org/10.1177/1082013203035518.
Full textAbstract:
Desiccation has many detrimental effects on the structure and function of biological membranes and proteins and this molecular damage decreases the freshness appearance of dehydrated foods. Phospholipid membranes are destabilised upon water stress by insertion of cellular amphiphiles, phase transition into the gel phase and membrane fusion. Proteins are denatured and electron transport chains are perturbed leading to increased formation of reactive oxygen species which cause irreversible damage of cellular structures. Cells respond to water stress by generating defense proteins and metabolites and eventually develop outstanding desiccation tolerance such as in the case of plant seeds and pollen, fungal spores, crustacean cysts, etc. The molecular bases for this remarkable phenomenon are not completely understood but several important principles have been identified. Three biological systems seem to act in concert to achieve desiccation tolerance: enzymes involved in osmolyte synthesis; proteins specialised in desiccation protection of membranes and proteins (LEA proteins), and antioxidant enzymes and molecules. Both osmolytes and LEA proteins contribute to stabilisation of membrane and protein structures by conferring preferential hydration at moderate desiccation and replacing water at extreme desiccation. Osmolytes also contribute to osmotic adjustment and act as hydroxyl radical scavengers. Genetically modified plants with increased production of these defenses could be useful to improve the quality of dried food.
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Johnson, Ross G., Tze-Hong Lu, Kathleen Klukas, Larry Takemoto, and S. Barbara Yancey. "Immunological approaches to gap junctions: Studies of immuno-localization, membrane protein topology, and function." Proceedings, annual meeting, Electron Microscopy Society of America 47 (August 6, 1989): 812–13. http://dx.doi.org/10.1017/s0424820100156031.
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It is now widely accepted that the plasma membranes of epithelial cells display a marked degree of polarity. This polarity is reflected in a number of parameters, e.g. the localization of certain proteins to basolateral membranes. Polarity is also illustrated by the presence of discrete membrane specializations, including desmosomes, tight junctions and gap junctions. These specializations provide strong support for the idea of membrane "domains" within the polarized membrane of the epithelial cell. This presentation relates to the proteins found in gap junction membranes. The issues include a clear identification of these proteins in different cells and an analysis of how a cell-to-cell channel is constructed by these proteins.The plasma membranes of most animal cells contain cell-to-cell channels, which provide for the direct, passive exchange of small molecules between cells. Collections of these channels are identified as "gap junctions." This form of intercellular communication is thought to be important in a wide variety of biological processes, including cellular differentiation, proliferation, and tissue homeostasis.
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Kufareva, Irina, Marc Lenoir, Felician Dancea, Pooja Sridhar, Eugene Raush, Christin Bissig, Jean Gruenberg, Ruben Abagyan, and Michael Overduin. "Discovery of novel membrane binding structures and functions." Biochemistry and Cell Biology 92, no. 6 (December 2014): 555–63. http://dx.doi.org/10.1139/bcb-2014-0074.
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The function of a protein is determined by its intrinsic activity in the context of its subcellular distribution. Membranes localize proteins within cellular compartments and govern their specific activities. Discovering such membrane-protein interactions is important for understanding biological mechanisms and could uncover novel sites for therapeutic intervention. We present a method for detecting membrane interactive proteins and their exposed residues that insert into lipid bilayers. Although the development process involved analysis of how C1b, C2, ENTH, FYVE, Gla, pleckstrin homology (PH), and PX domains bind membranes, the resulting membrane optimal docking area (MODA) method yields predictions for a given protein of known three-dimensional structures without referring to canonical membrane-targeting modules. This approach was tested on the Arf1 GTPase, ATF2 acetyltransferase, von Willebrand factor A3 domain, and Neisseria gonorrhoeae MsrB protein and further refined with membrane interactive and non-interactive FAPP1 and PKD1 pleckstrin homology domains, respectively. Furthermore we demonstrate how this tool can be used to discover unprecedented membrane binding functions as illustrated by the Bro1 domain of Alix, which was revealed to recognize lysobisphosphatidic acid (LBPA). Validation of novel membrane-protein interactions relies on other techniques such as nuclear magnetic resonance spectroscopy (NMR), which was used here to map the sites of micelle interaction. Together this indicates that genome-wide identification of known and novel membrane interactive proteins and sites is now feasible and provides a new tool for functional annotation of the proteome.
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Stoilova-McPhie, Svetla. "Lipid nanotechnologies for structural studies of membrane-associated clotting proteins by cryo-electron microscopy." Nanotechnology Reviews 6, no. 1 (February 1, 2017): 127–37. http://dx.doi.org/10.1515/ntrev-2016-0066.
Full textAbstract:
AbstractBiological membranes surround all living cells, confining internal organelles and participating in a variety of essential cellular functions, such as signaling, electrolyte balance, and energy conversion. Cell membranes are structurally and chemically heterogeneous environment composed of numerous types of lipids arranged as a continuous bilayer. The assembly of protein complexes at the membrane surface is responsible for fundamental biological processes such as synaptic transmission, blood coagulation, and apoptosis. Resolving the macromolecular organization of these complexes at the membrane surface will help to understand the structural basis of their function and significance for the associated biological processes. In this review, we present our work on direct structure determination of membrane-bound clotting factors, specifically factor VIII (FVIII), by cryogenic electron microscopy (CryoEM). To resolve the FVIII membrane-bound organization, we have optimized lipid nanostructures resembling the activated platelet membrane. Combining structural CryoEM, capable of near-atomic resolution, with customized lipid nanotechnologies is a powerful approach to investigate how the cellular membrane can modulate protein function at close to physiological conditions. The outcome will open novel avenues for developing lipid nanotechnologies of diverse shapes and composition that can be optimized for various protein systems, germane for both drug delivery and macromolecular structure determination.
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Harder, T., R. Kellner, R. G. Parton, and J. Gruenberg. "Specific release of membrane-bound annexin II and cortical cytoskeletal elements by sequestration of membrane cholesterol." Molecular Biology of the Cell 8, no. 3 (March 1997): 533–45. http://dx.doi.org/10.1091/mbc.8.3.533.
Full textAbstract:
Annexin II is an abundant protein which is present in the cytosol and on the cytoplasmic face of plasma membrane and early endosomes. It is generally believed that this association occurs via Ca(2+)-dependent binding to lipids, a mechanism typical for the annexin protein family. Although previous studies have shown that annexin II is involved in early endosome dynamics and organization, the precise biological role of the protein is unknown. In this study, we found that approximately 50% of the total cellular annexin was associated with membranes in a Ca(2+)-independent manner. This binding was extremely tight, since it resisted high salt and, to some extent, high pH treatments. We found, however, that membrane-associated annexin II could be quantitatively released by low concentrations of the cholesterol-sequestering agents filipin and digitonin. Both treatments released an identical and limited set of proteins but had no effects on other membrane-associated proteins. Among the released proteins, we identified, in addition to annexin II itself, the cortical cytoskeletal proteins alpha-actinin, ezrin and moesin, and membrane-associated actin. Our biochemical and immunological observations indicate that these proteins are part of a complex containing annexin II and that stability of the complex is sensitive to cholesterol sequestering agents. Since annexin II is tightly membrane-associated in a cholesterol-dependent manner, and since it seems to interact physically with elements of the cortical actin cytoskeleton, we propose that the protein serves as interface between membranes containing high amounts of cholesterol and the actin cytoskeleton.